2ZS0

Structural Basis for the Heterotropic and Homotropic Interactions of Invertebrate Giant Hemoglobin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Basis for the Heterotropic and Homotropic Interactions of Invertebrate Giant Hemoglobin

Numoto, N.Nakagawa, T.Kita, A.Sasayama, Y.Fukumori, Y.Miki, K.

(2008) Biochemistry 47: 11231-11238

  • DOI: 10.1021/bi8012609
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The oxygen binding properties of extracellular giant hemoglobins (Hbs) in some annelids exhibit features significantly different from those of vertebrate tetrameric Hbs. Annelid giant Hbs show cooperative oxygen binding properties in the presence of ...

    The oxygen binding properties of extracellular giant hemoglobins (Hbs) in some annelids exhibit features significantly different from those of vertebrate tetrameric Hbs. Annelid giant Hbs show cooperative oxygen binding properties in the presence of inorganic cations, while the cooperativities of vertebrate Hbs are enhanced by small organic anions or chloride ions. To elucidate the structural basis for the cation-mediated cooperative mechanisms of these giant Hbs, we determined the crystal structures of Ca2+- and Mg2+-bound Hbs from Oligobrachia mashikoi at 1.6 and 1.7 A resolution, respectively. Both of the metal-bound structures were determined in the oxygenated state. Four Ca2+-binding sites and one Mg2+-binding site were identified in each tetramer subassembly. These cations are considered to stabilize the oxygenated form and increase affinity and cooperativity for oxygen binding, as almost all of the Ca2+ and Mg2+ cations were bound at the interface regions, forming either direct or hydrogen bond-mediated interactions with the neighboring subunits. A comparison of the structures of the oxygenated form and the partially unliganded form provides structural insight into proton-coupled cooperativity (Bohr effect) and ligand-induced transitions. Two histidine residues are assumed to be primarily associated with the Bohr effect. With regard to the ligand-induced cooperativity, a novel quaternary rotation mechanism is proposed to exist at the interface region of the dimer subassembly. Interactions among conserved residues Arg E10, His F3, Gln F7, and Val E11, together with the bending motion of the heme molecules, appear to be essential for quaternary rearrangement.


    Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Kyoto UniVersity, Sakyo-ku, Kyoto 606-8502, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Extracellular giant hemoglobin major globin subunit A1
A
140Oligobrachia mashikoiMutation(s): 0 
Gene Names: ghbA1
Find proteins for Q7M419 (Oligobrachia mashikoi)
Go to UniProtKB:  Q7M419
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Extracellular giant hemoglobin major globin subunit A2
B
142Oligobrachia mashikoiMutation(s): 0 
Gene Names: ghbA2
Find proteins for Q7M413 (Oligobrachia mashikoi)
Go to UniProtKB:  Q7M413
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Extracellular giant hemoglobin major globin subunit B2
C
147Oligobrachia mashikoiMutation(s): 0 
Gene Names: ghbB2
Find proteins for Q7M418 (Oligobrachia mashikoi)
Go to UniProtKB:  Q7M418
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Extracellular giant hemoglobin major globin subunit B1
D
145Oligobrachia mashikoiMutation(s): 0 
Gene Names: ghbB1
Find proteins for Q5KSB7 (Oligobrachia mashikoi)
Go to UniProtKB:  Q5KSB7
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OXY
Query on OXY

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Download CCD File 
A, B, C, D
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
A, B, C, D
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.171 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 110.720α = 90.00
b = 110.720β = 90.00
c = 274.357γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction
BSSdata collection
MOLREPphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance